Plot counts per cell

Plot the disambiguated counts per cell.

Usage

plotCountsPerCell(object, ...)

# S4 method for SingleCellExperiment
plotCountsPerCell(
  object,
  geom = c("histogram", "ecdf", "violin", "ridgeline", "boxplot"),
  interestingGroups = NULL,
  min = 0L,
  max = Inf,
  point = c("none", "inflection", "knee"),
  trans = "log10",
  title = "Counts per cell"
)

Arguments

object

Object.

geom

character(1). Plot type. Uses match.arg() internally and defaults to the first argument in the character vector.

interestingGroups

character. Groups of interest to use for visualization. Corresponds to factors describing the columns of the object.

min

numeric(1). Recommended minimum value cutoff.

max

numeric(1). Recommended maximum value cutoff.

point

character(1). Label either the knee or inflection points per sample. Requires geom = "ecdf".

trans

character(1). Name of the axis scale transformation to apply.

For more information:

help(topic = "scale_x_continuous", package = "ggplot2")

title

character(1). Title.

...

Additional arguments.

Value

ggplot.

Details

"Counts" refer to universal molecular identifier (UMI) counts for droplet-based scRNA-seq data.

Note

Updated 2023-08-11.

Author

Michael Steinbaugh, Rory Kirchner

Examples

data(SingleCellExperiment_splatter, package = "AcidTest")

## SingleCellExperiment ====
object <- SingleCellExperiment_splatter
plotCountsPerCell(object, geom = "violin")

plotCountsPerCell(object, geom = "ridgeline")
#> Picking joint bandwidth of 0.0318

plotCountsPerCell(object, geom = "ecdf")

plotCountsPerCell(object, geom = "histogram")

plotCountsPerCell(object, geom = "boxplot")